IMPUTE

A computer program for phasing observed genotypes and imputing missing genotypes. IMPUTE increases accuracy and combines information across multiple reference panels while remaining computationally feasible. IMPUTE v2 attains higher accuracy than other methods when the HapMap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made.

[…] 907 autosomal SNPs.We then performed genotype imputation, using the phased haplotypes from the 1000 Genomes Project dataset as the reference panel. Prephasing and imputation was done with SHAPEIT and IMPUTE2,. The imputation was performed with the default parameters of the software. The final imputed dataset consisted of 9.7 million autosomal SNPs. […]

[…] a were cleaned according to the following QC criteria: sample/SNP call rate <98%, MAF<0.01, and HWE test P<10-6. After QC, the SNP genotypes were imputed to the 1000G (phase 1) reference panels using IMPUTE2 (Supplementary Table ). The imputed SNPs with imputation INFO scores <0.3, MAF<0.01, or HWE P<10-6 in any of the populations (AFR, EAS, and EUR) were removed (Supplementary Table ), resulting […]

[…] in order to remove poorly imputed markers that might have adverse effects on the imputation procedures.Imputation from 54 k to HD genotypes to HD and imputation to the WGS level were undertaken with IMPUTE2 v2.3.1 [] and Minimac2 [], respectively. The imputation to whole genome sequence was done in chunks of 5 Mb with the length of buffer region of 0.25 Mb on either side. A total of 22,751,039 bi […]

[…] inberg equilibrium (HWE) (p IMPUTE v2.3.2 using a merged reference panel consisting of data from phase three of the 1,000 genomes project and the UK10K–.TCGA cases were genotyped on the Affymetrix Genomewide 6.0 array using DNA […]

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